At-sea shifts in food quality and availability can affect populations of marine birds; however, it is difficult to evaluate the impacts of changes in prey composition and availability without some baseline information on diet composition. The little penguin (Eudyptula minor) is a common inshore-feeding seabird in New Zealand and Australia. To date, only two dietary studies have been undertaken on the little penguin in New Zeaalnd, at two widely separated locations. This study recorded diet of little penguins during the chick-rearing stage of breeding at three colonies in southern New Zealand. Sixty-nine stomach samples were acquired via the stomach flushing technique at Banks Peninsula, Oamaru, and Stewart Island. Prey composition differed between each site: (1) at Oamaru, Graham’s gudgeon (Grahamichthys radiata) occurred most frequently (100%) and contributed the most to meal mass (92.1%); (2) at Banks Peninsula arrow squid (Nototodarus sloanii) occurred most frequently (87.5%), but two fish species – slender sprat (Sprattus antipodum) (33.9%) and ahuru (Auchenoceros punctatus) (37.4%) – contributed most to meal mass; and (3) at Stewart Island arrow squid occurred most frequently (91.3%), and contributed most to meal mass (73.1%). Little penguins take a wide diversity of species, and may switch between species, probably in response to temporal variation in availability. In New Zealand, little penguins ate higher proportions of lower quality cephalopods than those in Australia. As top predators in the marine ecosystem, changes in little penguin diet may indicate changes occurring in the inshore marine ecosystem.